In Ontario, as a charity, we are entitled to a rebate of our HST on the following basis:
Federal portion of HST (ie 5%) – 50% rebate, ie 2.5% of the sales amount
Provincial portion of HST (ie 8%) – 82% rebate, ie 6.56% of the sales amount
So I have set up my accounting system to automatically split HST payments into four accounts:
The first two are asset accounts, ie receivables:
– Federal portion of HST – refundable (2.5%)
– Provincial portion of HST – refundable (6.56%)
These accumulate until the time to submit the request for the rebate (in our case, twice a year) and then the amounts are exactly what is needed to fill out the form.
The second two are expense accounts:
– Federal portion of HST – nonrefundable (2.5%)
– Provincial portion of HST – nonrefundable (1.44%)
These four percents add up to 13%, which is the current HST paid in Ontario.
When the refund cheque is received, the entry is a debit in bank account and a credit to each of the HST refundable accounts.

British Columbia – HST 12%
Under Revenue I have set up an account – HST Refund
Under General & Administrative Expenses I have set up an account – HST Paid on Purchases
We are entitled to a 50% rebate on the the Federal portion and I’m not sure what the Provincial portion is.
There is probably a better way to set this up but I just did it real simple.

Thanks all for your replies. I’m clear now that this isn’t relevant for charities and churches in the USA, which are tax-exempt. I’ve written a longing Help page on Handling Sales Tax for those of you in Canada – it will be in the next beta test version.